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Bacterial whole genome sequencing

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https://www.readbyqxmd.com/read/28550057/prevalence-and-genomic-characterization-of-escherichia-coli-o157-h7-in-cow-calf-herds-throughout-california
#1
Jay N Worley, Kristopher A Flores, Xun Yang, Jennifer A Chase, Guojie Cao, Shuai Tang, Jianghong Meng, Edward R Atwill
Escherichia coli serotype O157:H7 (E. coli O157:H7) is a zoonotic food- and waterborne bacterial pathogen that has a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, like cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle present food safety challenges on a uniquely large scale...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28541480/alternative-evolutionary-paths-to-bacterial-antibiotic-resistance-cause-distinct-collateral-effects
#2
C Barbosa, V Trebosc, C Kemmer, P Rosenstiel, R Beardmore, H Schulenburg, G Jansen
When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To date, the presence and molecular basis of collateral sensitivity has only been studied in few bacterial species and is unknown for opportunistic human pathogens such as Pseudomonas aeruginosa. In the present study, we assessed patterns of collateral effects by experimentally evolving 160 independent populations of P...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535774/a-bacterial-negative-transcription-regulator-binding-on-an-inverted-repeat-in-the-promoter-for-epothilone-biosynthesis
#3
Xin-Jing Yue, Xiao-Wen Cui, Zheng Zhang, Ran Peng, Peng Zhang, Zhi-Feng Li, Yue-Zhong Li
BACKGROUND: Microbial secondary metabolism is regulated by a complex and mostly-unknown network of global and pathway-specific regulators. A dozen biosynthetic gene clusters for secondary metabolites have been reported in myxobacteria, but a few regulation factors have been identified. RESULTS: We identified a transcription regulator Esi for the biosynthesis of epothilones. Inactivation of esi promoted the epothilone production, while overexpression of the gene suppressed the production...
May 23, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28531216/impact-of-mutations-in-toll-like-receptor-pathway-genes-on-esophageal-carcinogenesis
#4
Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O'Donovan, Nick J Gay, Rebecca C Fitzgerald
Esophageal adenocarcinoma (EAC) develops in an inflammatory microenvironment with reduced microbial diversity, but mechanisms for these influences remain poorly characterized. We hypothesized that mutations targeting the Toll-like receptor (TLR) pathway could disrupt innate immune signaling and promote a microenvironment that favors tumorigenesis. Through interrogating whole genome sequencing data from 171 EAC patients, we showed that non-synonymous mutations collectively affect the TLR pathway in 25/171 (14...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28521002/changes-in-microbiome-during-and-after-travellers-diarrhea-what-we-know-and-what-we-do-not
#5
David A Rasko
The study of bacterial pathogens has advanced from culture on plates to basic biochemical studies; to sequencing reference genomes and attempting to ascribe those qualities to the whole species; to evaluating complete communities based on the universal marker of the 16S rRNA gene; to now sequencing all available nucleic acids in any sample to characterize the community as a whole. These types of scientific advances highlight that there are multiple layers of information within any sample, and to some extent we are only now beginning to be able to identify, categorize and understand the complex interactions of the host, pathogen and microbiome...
April 1, 2017: Journal of Travel Medicine
https://www.readbyqxmd.com/read/28516866/invasive-serotype-35b-pneumococci-including-an-expanding-serotype-switch-lineage-united-states-2015-2016
#6
Sopio Chochua, Benjamin J Metcalf, Zhongya Li, Hollis Walker, Theresa Tran, Lesley McGee, Bernard Beall
We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015-2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post-pneumococcal 7-valent conjugate vaccine years (2001-2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28493321/local-genes-for-local-bacteria-evidence-of-allopatry-in-the-genomes-of-transatlantic-campylobacter-populations
#7
Ben Pascoe, Guillaume Méric, Koji Yahara, Helen Wimalarathna, Susan Murray, Matthew D Hitchings, Emma L Sproston, Catherine D Carrillo, Eduardo N Taboada, Kerry K Cooper, Steven Huynh, Alison J Cody, Keith A Jolley, Martin C J Maiden, Noel D McCarthy, Xavier Didelot, Craig T Parker, Samuel K Sheppard
The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin...
May 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28475792/clinical-and-molecular-epidemiology-of-carbapenem-resistant-enterobacteriaceae-among-adult-inpatients-in-singapore
#8
Kalisvar Marimuthu, Indumathi Venkatachalam, Wei Xin Khong, Tse Hsien Koh, Benjamin Pei Zhi Cherng, My Van La, Partha Pratim De, Prabha Unny Krishnan, Thean Yen Tan, Raymond Fong Kok Choon, Surinder Kaur Pada, Choong Weng Lam, Say Tat Ooi, Rama Narayana Deepak, Nares Smitasin, Eng Lee Tan, Jia Jun Lee, Asok Kurup, Barnaby Young, Nancy Tee Wen Sim, Koh Cheng Thoon, Dale Fisher, Moi Lin Ling, Brenda Ang Sze Peng, Yik-Ying Teo, Li Yang Hsu, Raymond Tzer Pin Lin, Rick Twee-Hee Ong, Jeanette Teo, Oon Tek Ng
Background: Since 2010, the incidence of carbapenem-resistant Enterobacteriaceae (CRE) has been increasing in Singapore. We analyzed the clinical and molecular epidemiology of CRE among adult inpatients in Singapore. Methods: Quarterly incidence of unique subjects (per 100000 patient-days) with positive clinical and surveillance cultures for CRE were estimated based on mandatory data submitted to the National Public Health Laboratory by public hospitals between 2010 and 2015...
May 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28475781/2015-epidemic-of-severe-streptococcus-agalactiae-sequence-type-283-infections-in-singapore-associated-with-the-consumption-of-raw-freshwater-fish-a-detailed-analysis-of-clinical-epidemiological-and-bacterial-sequencing-data
#9
Shirin Kalimuddin, Swaine L Chen, Cindy T K Lim, Tse Hsien Koh, Thean Yen Tan, Michelle Kam, Christopher W Wong, Kurosh S Mehershahi, Man Ling Chau, Lee Ching Ng, Wen Ying Tang, Hishamuddin Badaruddin, Jeanette Teo, Anucha Apisarnthanarak, Nuntra Suwantarat, Margaret Ip, Matthew T G Holden, Li Yang Hsu, Timothy Barkham
Background: Streptococcus agalactiae (group B Streptococcus [GBS]) has not been described as a foodborne pathogen. However, in 2015, a large outbreak of severe invasive sequence type (ST) 283 GBS infections in adults epidemiologically linked to the consumption of raw freshwater fish occurred in Singapore. We attempted to determine the scale of the outbreak, define the clinical spectrum of disease, and link the outbreak to contaminated fish. Methods: Time-series analysis was performed on microbiology laboratory data...
May 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28473817/comprehensive-diagnosis-of-bacterial-infection-associated-with-acute-cholecystitis-using-metagenomic-approach
#10
Manabu Kujiraoka, Makoto Kuroda, Koji Asai, Tsuyoshi Sekizuka, Kengo Kato, Manabu Watanabe, Hiroshi Matsukiyo, Tomoaki Saito, Tomotaka Ishii, Natsuya Katada, Yoshihisa Saida, Shinya Kusachi
Acute cholecystitis (AC), which is strongly associated with retrograde bacterial infection, is an inflammatory disease that can be fatal if inappropriately treated. Currently, bacterial culture testing, which is basically recommended to detect the etiological agent, is a time-consuming (4-6 days), non-comprehensive approach. To rapidly detect a potential pathogen and predict its antimicrobial susceptibility, we undertook a metagenomic approach to characterize the bacterial infection associated with AC. Six patients (P1-P6) who underwent cholecystectomy for AC were enrolled in this study...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28473387/draft-genome-sequence-of-gardnerella-vaginalis-strain-atcc-49145-associated-with-bacterial-vaginosis
#11
Destaalem T Kidane, Brock A Arivett, Jacob Crigler, Eric J Vick, Anthony L Farone, Mary B Farone
Gardnerella vaginalis is a Gram-variable bacterium associated with bacterial vaginosis, a common vaginal inflammation in women of reproductive age. This study reports the whole-genome sequencing for the clinical isolate strain ATCC 49145. The draft genome is composed of 21 contigs containing 1,325 protein-coding sequences, 45 tRNAs and a single tmRNA (SsrA).
May 4, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28472260/whole-genome-sequencing-accurately-identifies-resistance-to-extended-spectrum-%C3%AE-lactams-for-major-gram-negative-bacterial-pathogens
#12
Samuel A Shelburne, Jiwoong Kim, Jose M Munita, Pranoti Sahasrabhojane, Ryan K Shields, Ellen G Press, Xiqi Li, Cesar A Arias, Brandi Cantarel, Ying Jiang, Min S Kim, Samuel L Aitken, David E Greenberg
Background: There is marked interest in using DNA based methods to detect antimicrobial resistance (AMR) with targeted polymerase chain reaction (PCR) approaches increasingly being incorporated into clinical care. Whole genome sequencing (WGS) could offer significant advantages over targeted PCR for AMR detection, particularly for species where mutations are major drivers of AMR. Methods: Illumina MiSeq WGS and broth microdilution (BMD) assays were performed on 90 bloodstream isolates of the four most common gram-negative bacteria causing bloodstream infections in neutropenic patients...
May 3, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28468851/whole-genome-sequencing-reveals-the-contribution-of-long-term-carriers-in-staphylococcus-aureus-outbreak-investigation
#13
N C Gordon, B Pichon, T Golubchik, D J Wilson, J Paul, D S Blanc, K Cole, J Collins, N Cortes, M Cubbon, F K Gould, P J Jenks, M Llewelyn, J Q Nash, J M Orendi, K Paranthaman, J Price, L Senn, H L Thomas, S Wyllie, D W Crook, T E A Peto, A S Walker, A M Kearns
Whole genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at high resolution, helping to characterise outbreaks. However, for Staphylococcus aureus, accumulation of within-host diversity during carriage might limit interpretation of sequencing data.In this study, we hypothesised the converse: that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analysed WGS data from 20 historical outbreaks, and applied phylogenetic methods to assess genetic relatedness and estimate time to most recent common ancestor (TMRCA)...
May 3, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28467925/gut-microbiome-based-metagenomic-signature-for-non-invasive-detection-of-advanced-fibrosis-in-human-nonalcoholic-fatty-liver-disease
#14
Rohit Loomba, Victor Seguritan, Weizhong Li, Tao Long, Niels Klitgord, Archana Bhatt, Parambir Singh Dulai, Cyrielle Caussy, Richele Bettencourt, Sarah K Highlander, Marcus B Jones, Claude B Sirlin, Bernd Schnabl, Lauren Brinkac, Nicholas Schork, Chi-Hua Chen, David A Brenner, William Biggs, Shibu Yooseph, J Craig Venter, Karen E Nelson
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis)...
May 2, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28462035/whole-genome-sequencing-of-group-a-streptococcus-development-and-evaluation-of-an-automated-pipeline-for-emmgene-typing
#15
Georgia Kapatai, Juliana Coelho, Steven Platt, Victoria J Chalker
Streptococcus pyogenes group A Streptococcus (GAS) is the most common cause of bacterial throat infections, and can cause mild to severe skin and soft tissue infections, including impetigo, erysipelas, necrotizing fasciitis, as well as systemic and fatal infections including septicaemia and meningitis. Estimated annual incidence for invasive group A streptococcal infection (iGAS) in industrialised countries is approximately three per 100,000 per year. Typing is currently used in England and Wales to monitor bacterial strains of S...
2017: PeerJ
https://www.readbyqxmd.com/read/28461450/a-mutation-in-the-bacillus-subtilis-rsbu-gene-that-limits-rna-synthesis-during-sporulation
#16
David M Rothstein, David Lazinski, Marcia S Osburne, Abraham L Sonenshein
Mutants of Bacillis subtilis that are temperature-sensitive for RNA synthesis during sporulation were isolated after (32)P-suicide selection. Whole genome sequencing revealed that two of the mutants carried the identical lesion in the rsbU gene, which encodes a phosphatase that indirectly activates SigB, the stress-responsive RNA polymerase sigma factor. The mutation appeared to cause RsbU to be hyperactive, because the mutants were more resistant than the parent strain to ethanol stress. In support of this hypothesis, pseudorevertants that regained wild-type levels of sporulation at high temperature had secondary mutations that prevented expression of the mutant rsbU gene...
May 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28458658/delineation-of-taxonomic-species-within-complex-of-species-aeromonas-media-and-related-species-as-a-test-case
#17
Emilie Talagrand-Reboul, Frédéric Roger, Jean-Luc Kimper, Sophie M Colston, Joerg Graf, Fadua Latif-Eugenín, Maria José Figueras, Fabienne Petit, Hélène Marchandin, Estelle Jumas-Bilak, Brigitte Lamy
Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28446571/a-core-genome-multi-locus-sequence-typing-scheme-for-stable-comparative-analyses-of-campylobacter-jejuni-and-c-coli-human-disease-isolates
#18
Alison J Cody, James E Bray, Keith A Jolley, Noel D McCarthy, Martin C J Maiden
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterisation methods. Whole genome sequencing (WGS) data enables the improvement of sequence-based typing approaches, such as multi locus sequence typing (MLST), by substantially increasing the number of loci examined...
April 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28445510/whole-genome-re-sequencing-to-identify-suppressor-mutations-of-mutant-and-foreign-escherichia-coli-ftsz
#19
Kiani A J Arkus Gardner, Masaki Osawa, Harold P Erickson
FtsZ is an essential protein for bacterial cell division, where it forms the cytoskeletal scaffold and may generate the constriction force. We have found previously that some mutant and foreign FtsZ that do not complement an ftsZ null can function for cell division in E. coli upon acquisition of a suppressor mutation somewhere in the genome. We have now identified, via whole genome re-sequencing, single nucleotide polymorphisms in 11 different suppressor strains. Most of the mutations are in genes of various metabolic pathways, which may modulate cell division indirectly...
2017: PloS One
https://www.readbyqxmd.com/read/28424528/elucidation-of-quantitative-structural-diversity-of-remarkable-rearrangement-regions-shufflons-in-inci2-plasmids
#20
Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing...
April 19, 2017: Scientific Reports
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